PyMFEM
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mfem
Up-to-date installation for parallel version?
Installying PyMFEM with pip install mfem --install-option="--with-parallel" does not work any longer, since --install-option became deprecated due to the recent update. I tried to follow the other option of cloning the repo and using setup.py, but it also fails with the following message:
calling ... /usr/local/bin/swig -Wall -c++ -python -fastproxy -olddefs -keyword -I/usr/local/lib/python3.10/dist-packages/mfem/external/par/include -I/usr/local/lib/python3.10/dist-packages/mfem/external/par/include/mfem -I/home/test/PyMFEM/external/mfem -I/usr/local/lib/python3.10/dist-packages/mfem/external/include -I/usr/local/lib/python3.10/dist-packages/mfem/external/include -I/usr/local/lib/python3.10/dist-packages/mpi4py/include blockmatrix.i
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/usr/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/home/test/PyMFEM/setup.py", line 314, in make_call
raise subprocess.CalledProcessError(p.returncode,
subprocess.CalledProcessError: Command '/usr/local/bin/swig -Wall -c++ -python -fastproxy -olddefs -keyword -I/usr/local/lib/python3.10/dist-packages/mfem/external/par/include -I/usr/local/lib/python3.10/dist-packages/mfem/external/par/include/mfem -I/home/test/PyMFEM/external/mfem -I/usr/local/lib/python3.10/dist-packages/mfem/external/include -I/usr/local/lib/python3.10/dist-packages/mfem/external/include -I/usr/local/lib/python3.10/dist-packages/mpi4py/include dist_solver.i' returned non-zero exit status 1.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/test/PyMFEM/setup.py", line 1881, in <module>
main()
File "/home/test/PyMFEM/setup.py", line 1877, in main
run_setup()
File "/home/test/PyMFEM/setup.py", line 1865, in run_setup
setup(
File "/usr/lib/python3/dist-packages/setuptools/__init__.py", line 153, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.10/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.10/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/test/PyMFEM/setup.py", line 1662, in run
_install.run(self)
File "/usr/lib/python3/dist-packages/setuptools/command/install.py", line 72, in run
orig.install.run(self)
File "/usr/lib/python3.10/distutils/command/install.py", line 619, in run
self.run_command('build')
File "/usr/lib/python3.10/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/usr/lib/python3.10/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python3.10/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/home/test/PyMFEM/setup.py", line 1717, in run
generate_wrapper()
File "/home/test/PyMFEM/setup.py", line 1099, in generate_wrapper
mp_pool.map(make_call, commands)
File "/usr/lib/python3.10/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/usr/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
subprocess.CalledProcessError: Command '/usr/local/bin/swig -Wall -c++ -python -fastproxy -olddefs -keyword -I/usr/local/lib/python3.10/dist-packages/mfem/external/par/include -I/usr/local/lib/python3.10/dist-packages/mfem/external/par/include/mfem -I/home/test/PyMFEM/external/mfem -I/usr/local/lib/python3.10/dist-packages/mfem/external/include -I/usr/local/lib/python3.10/dist-packages/mfem/external/include -I/usr/local/lib/python3.10/dist-packages/mpi4py/include dist_solver.i' returned non-zero exit status 1.
What is the most up-to-date installation procedure for parallel PyMFEM?
An update: I tried to install the parallel version with
git clone https://github.com/mfem/PyMFEM.git
cd PyMFEM
python3 setup.py install --with-parallel
It seems to successfully build PyMFEM with the following output:
...
byte-compiling /usr/lib/python3.10/site-packages/mfem/_ser/mem_manager.py to mem_manager.cpython-310.pyc
byte-compiling /usr/lib/python3.10/site-packages/mfem/_ser/sort_pairs.py to sort_pairs.cpython-310.pyc
running install_egg_info
running egg_info
creating mfem.egg-info
writing mfem.egg-info/PKG-INFO
writing dependency_links to mfem.egg-info/dependency_links.txt
writing requirements to mfem.egg-info/requires.txt
writing top-level names to mfem.egg-info/top_level.txt
writing manifest file 'mfem.egg-info/SOURCES.txt'
reading manifest file 'mfem.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'external/README.txt'
adding license file 'LICENSE'
writing manifest file 'mfem.egg-info/SOURCES.txt'
Copying mfem.egg-info to /usr/lib/python3.10/site-packages/mfem-4.5.2.0-py3.10.egg-info
running install_scripts
test@9a0a7bde1732:~/PyMFEM$
However, importing it on python shell throws the following error:
test@9a0a7bde1732:~$ python3
Python 3.10.6 (main, May 29 2023, 11:10:38) [GCC 11.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import mfem
>>> mfem.__path__
['/usr/lib/python3.10/site-packages/mfem']
>>> import mfem.par as mfem
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.10/site-packages/mfem/par.py", line 12, in <module>
from mfem._par.globals import *
File "/usr/lib/python3.10/site-packages/mfem/_par/globals.py", line 10, in <module>
from . import _globals
ImportError: libmfem.so.4.5.2: cannot open shared object file: No such file or directory
When I looked into /usr/lib/python3.10/site-packages/mfem, I could not find the libmfem.so.4.5.2 file.
Attached is the entire log of the python command I tried above. It finished without any error, but having an import error within python as reported above. pymfem.log
Another update I was able to install parallel PyMFEM with the following command:
python3 setup.py install --with-parallel --user
The default command python3 setup.py install --with-parallel has a problem when run on Debian/Ubuntu. In the pymfem.log attached above, all the paths are set to dist-packages directory:
ext_prefix running external_install_prefix with the following parameters sys.argv : ['setup.py', 'install', '--with-parallel'] sys.prefix : /usr usersite : /root/.local/lib/python3.10/site-packages prefix : /usr ----configuration---- prefix /usr when needed, the dependency (mfem/hypre/metis) will be installed under /usr/local/lib/python3.10/dist-packages/mfem/external build mfem : Yes build metis : Yes build hypre : Yes build libceed : No build gslib : No call SWIG wrapper generator: Yes build serial wrapper: Yes build parallel wrapper : Yes hypre prefix /usr/local/lib/python3.10/dist-packages/mfem/external metis prefix /usr/local/lib/python3.10/dist-packages/mfem/external c compiler : cc c++ compiler : c++ mpi-c compiler : mpicc mpi-c++ compiler : mpic++ verbose : No SWIG : /usr/local/bin/swig
However, at the last steps of installation, the files are installed to site-packages directory:
byte-compiling /usr/lib/python3.10/site-packages/mfem/_ser/hash.py to hash.cpython-310.pyc byte-compiling /usr/lib/python3.10/site-packages/mfem/_ser/socketstream.py to socketstream.cpython-310.pyc byte-compiling /usr/lib/python3.10/site-packages/mfem/_ser/mem_manager.py to mem_manager.cpython-310.pyc byte-compiling /usr/lib/python3.10/site-packages/mfem/_ser/sort_pairs.py to sort_pairs.cpython-310.pyc running install_egg_info running egg_info creating mfem.egg-info writing mfem.egg-info/PKG-INFO writing dependency_links to mfem.egg-info/dependency_links.txt writing requirements to mfem.egg-info/requires.txt writing top-level names to mfem.egg-info/top_level.txt writing manifest file 'mfem.egg-info/SOURCES.txt' reading manifest file 'mfem.egg-info/SOURCES.txt' reading manifest template 'MANIFEST.in' warning: no files found matching 'external/README.txt' adding license file 'LICENSE' writing manifest file 'mfem.egg-info/SOURCES.txt' Copying mfem.egg-info to /usr/lib/python3.10/site-packages/mfem-4.5.2.0-py3.10.egg-info running install_scripts
It seems that using --user unifies all the paths to site-packages, however not all the paths are set correctly when --user is not used.
I think there are some path mismatches in case of not using --user, particularly in _install_lib and _install_egg_info. Would it be possible to be fixed? We would want to not use --user so that PyMFEM is accessible to all users in the system.
@sshiraiwa , is it okay to invite me to this repo? I think I found a fix for this, but could not make a pull request due to permission issue.
Are there any updates on this? I can't get PyMFEM built with parallel on either Linux or MacOS right now. On Linux I'm having issues with CMake, but on MacOS, I execute
python3 setup.py install --with-parallel
and it breaks with:
Failed when calling command: /usr/local/opt/[email protected]/bin/python3.11 generate_lininteg_ext.py
Traceback (most recent call last):
File "/Users/lyons/src/PyMFEM/setup.py", line 1894, in <module>
main()
File "/Users/lyons/src/PyMFEM/setup.py", line 1890, in main
run_setup()
File "/Users/lyons/src/PyMFEM/setup.py", line 1878, in run_setup
setup(
File "/usr/local/lib/python3.11/site-packages/setuptools/__init__.py", line 103, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python3.11/site-packages/setuptools/dist.py", line 963, in run_command
super().run_command(command)
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/lyons/src/PyMFEM/setup.py", line 1675, in run
_install.run(self)
File "/usr/local/lib/python3.11/site-packages/setuptools/command/install.py", line 82, in run
orig.install.run(self)
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/command/install.py", line 697, in run
self.run_command('build')
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.11/site-packages/setuptools/dist.py", line 963, in run_command
super().run_command(command)
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 131, in run
self.run_command(cmd_name)
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.11/site-packages/setuptools/dist.py", line 963, in run_command
super().run_command(command)
File "/usr/local/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/lyons/src/PyMFEM/setup.py", line 1730, in run
generate_wrapper()
File "/Users/lyons/src/PyMFEM/setup.py", line 1058, in generate_wrapper
update_integrator_exts()
File "/Users/lyons/src/PyMFEM/setup.py", line 1011, in update_integrator_exts
make_call(command1)
File "/Users/lyons/src/PyMFEM/setup.py", line 319, in make_call
raise subprocess.CalledProcessError(p.returncode,
subprocess.CalledProcessError: Command '/usr/local/opt/[email protected]/bin/python3.11 generate_lininteg_ext.py' returned non-zero exit status 1.
When I re-execute the offending command, I get:
>/usr/local/opt/[email protected]/bin/python3.11 generate_lininteg_ext.py
WhiteGaussianNoiseDomainLFIntegrator
def __init__(self, seed_=0):
Traceback (most recent call last):
File "/Users/lyons/src/PyMFEM/mfem/common/generate_lininteg_ext.py", line 30, in <module>
assert False, "No recipt for this pattern "
AssertionError: No recipt for this pattern
I can open a separate issue if necessary.
